Results 1 to 10 of about 22,786 (211)

Scalable molecular dynamics with NAMD [PDF]

Journal of Computational Chemistry, 2005
AbstractNAMD is a parallel molecular dynamics code designed for high‐performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high‐end parallel platforms, as well as tens of processors on low‐cost commodity clusters, and also runs on individual desktop and laptop computers.
James C Phillips, Rosemary I Braun, James C Gumbart   +2 more
exaly   +3 more sources

NAMD goes quantum: an integrative suite for hybrid simulations [PDF]

Nature Methods, 2018
Hybrid methods that combine quantum mechanics (QM) and molecular mechanics (MM) can be applied to studies of reaction mechanisms in locations ranging from active sites of small enzymes to multiple sites in large bioenergetic complexes. By combining the widely used molecular dynamics and visualization programs NAMD and VMD with the quantum chemistry ...
Marcelo C R Melo, Rafael C Bernardi, Till Rudack   +2 more
exaly   +4 more sources

Scalable molecular dynamics on CPU and GPU architectures with NAMD

Journal of Chemical Physics, 2020
NAMD is a molecular dynamics program designed for high-performance simulations of very large biological objects on CPU- and GPU-based architectures. NAMD offers scalable performance on petascale parallel supercomputers consisting of hundreds of thousands of cores, as well as on inexpensive commodity clusters commonly found in academic environments.
James C Phillips, David J Hardy, Julio Daniel Carvalho Maia   +2 more
exaly   +5 more sources

Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD [PDF]

Computer Physics Communications, 2014
Computational methodologies that couple the dynamical evolution of a set of replicated copies of a system of interest offer powerful and flexible approaches to characterize complex molecular processes. Such multiple copy algorithms (MCAs) can be used to enhance sampling, compute reversible work and free energies, as well as refine transition pathways ...
Wei Jiang, James C Phillips, Lei Huang
exaly   +3 more sources

Histopathologic evidence of VEGF in early neovascular AMD: from a 1992 hypothesis to a 1994 discovery — a historical perspective [PDF]

International Journal of Retina and Vitreous
Background In the early1990s, neovascular age-related macular degeneration (nAMD) was the leading cause of irreversible vision loss in older adults, yet its molecular basis remained unknown.
K. Alexander Dastgheib
doaj   +2 more sources

Incidence, clinical features, risk factors, and outcomes of Intraocular inflammation following Brolucizumab in Indian eyes – A multicentric study

Indian Journal of Ophthalmology, 2023
Purpose: To report the incidence, clinical features, potential risk factors, and outcomes of intraocular inflammation (IOI) following brolucizumab in Indian eyes. Methods: All consecutive patients diagnosed with brolucizumab-induced IOI from 10 centers
Debdulal Chakraborty, Soumen Mondal, Sabyasachi Sengupta, Zahir Abbas, Khushboo Chandra, Subhendu Boral, Aniruddha Maiti, Sangeeta Roy, Angshuman Mukherjee, Arnab Das, Somnath Chakraborty, Pinaki Nag   +11 more
doaj   +1 more source

Software pipeline for predicting and analyzing the structure of the receptor–ligand

Учёные записки Казанского университета: Серия Физико-математические науки, 2022
It is of fundamental importance in pharmacology and theoretical biology to analyze the binding of ligands to receptors. A better understanding of this process and its outcomes can help predict the following: how the protein interacts with ligands ...
A.S. Kozlova, A.R. Mukhametgalieva, A.N. Fattakhova, N.I. Akberova   +3 more
doaj   +1 more source

Patterns of treatment discontinuation in patients receiving anti-vascular endothelial growth factor for neovascular age-related macular degeneration

Indian Journal of Ophthalmology, 2022
Purpose: To report the reasons for treatment discontinuation within 5 years in patients receiving intravitreal anti-vascular endothelial growth factor (anti-VEGF) therapy for neovascular age-related macular degeneration (nAMD).
Narendra Dhingra, Deepa Upasani, Faruque D Ghanchi   +2 more
doaj   +1 more source

Real-world experience of brolucizumab in nAMD

Indian Journal of Ophthalmology, 2023
Purpose: To evaluate real-world outcomes with neovascular age-related macular degeneration (nAMD) in relation to anatomical success, visual outcomes, and safety of intravitreal brolucizumab (IVBr) injection at 1.5 years. Methods: Prospective, randomized, single-center study between ...
Shilpi H Narnaware, Anju Bansal, Prashant K Bawankule, Dhananjay Raje   +3 more
openaire   +3 more sources

Pachychoroid neovasculopathy versus macular neovascularization in age-related macular degeneration with and without shallow irregular pigment epithelial detachment

Scientific Reports, 2023
To compare the choroidal neovascular features of individuals with pachychoroid neovasculopathy (PNV) and neovascular age-related macular degeneration (nAMD) with and without shallow irregular pigment epithelial detachment (SIPED). Using optical coherence
Hamid Riazi-Esfahani, Esmaeil Asadi Khameneh, Fariba Ghassemi, Mohammadreza Mehrabi Bahar, Ali torkashvand, Alireza Mahmoudi, Ahmed Husein Ahmed, Shahin Faghihi, Masoud Rahimi, Ali Akbarzadeh, Hooshang Faghihi, Elias Khalili Pour   +11 more
doaj   +1 more source